[gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 27

[Dallas Warren]

Include complete details about what you have done, additions you have
made to the files, the error you now obtain etc. Make it easier for
people to help, provide as much information, files and output you can.
That will speed things up, make it easier and more likely you'll get a
reply.

Did you edit the correct residuetypes.dat (i.e. if you have multiple
versions of GROMACS installed)?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Mon, 13 May 2019 at 23:33, Edjan Silva <edjan.silva at esenfar.ufal.br> wrote:
>
> HELP - Fatal error gmx pdb2gmx (Justin Lemkul)
>
> Yes. Includes residues in residuetypes.dat. however the same error remains.
>
> >    2. Re: HELP - Fatal error gmx pdb2gmx (Justin Lemkul)
> > Message: 2
> > Date: Fri, 10 May 2019 18:00:09 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] HELP - Fatal error gmx pdb2gmx
> > Message-ID: <88dab19b-d590-c2dd-8dbb-7ec9ab4ab417 at vt.edu>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> >
> >
> > On 5/10/19 2:26 PM, Edjan Silva wrote:
> > > I deleted all non-protein molecules and saved the file. I typed the
> > > following command:
> > >
> > > *gmx pdb2gmx -f 4gy7.pdb -o conf.gro -ignh*
> > >
> > > The error was as follows:
> > >
> > > *Fatal error:*
> > > *The residues in the chain MET1--PHE840 do not have a consistent type.
> > The*
> > > *first residue has type 'Protein', while residue CME59 is of type
> > 'Other'.*
> > > *Either there is a mistake in your chain, or it includes nonstandard
> > > residue*
> > > *names that have not yet been added to the residuetypes.dat file in the
> > > GROMACS*
> > > *library directory. If there are other molecules such as ligands, they
> > > should*
> > > *not have the same chain ID as the adjacent protein chain since it's a
> > > separate*
> > > *molecule.*
> > >
> > > *For more information and tips for troubleshooting, please check the
> > > GROMACS*
> > > *website at http://www.gromacs.org/Documentation/Errors
> > > <http://www.gromacs.org/Documentation/Errors>*
> > >
> > > I could not run the command without problem. What should I do?
> >
> > Have you tried following what the error says by adding the nonstandard
> > residue to residuetypes.dat?
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> >
> >
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> > End of gromacs.org_gmx-users Digest, Vol 181, Issue 27
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